Microbiology Commons^™

Fungal Diversity In Lespedeza Cuneata Roots, Gwendolyn Happ, Sophia Mcdade, Anthony Yannarell

MICRO-CCS student projects

Background

• Plants form a relationship with fungi that can be beneficial or harmful
• Fungi may grow on the plant surface, within plant tissues, or around roots
• Plants release compounds that invite fungi to their roots and chemicals  that can diminish unwanted fungi

Why Lespedeza cuneata? 

• Invasive that competes with native plants and damages biodiversity within plant and animal communities
• Alters soil microbiome
• Expansive seed bank and deep root system
• Understanding its microbiome can help in understanding invasive species success and ecology

Validation Of A Real-Time Pcr Laboratory Developed Test For The Detection Of Pneumocystis Jirovecii In Bronchoalveolar Lavage Samples, Caitlyn Moon

Honors Scholar Theses

Pneumocystis jirovecii is an opportunistic, host-obligate fungal pathogen responsible for causing P. jirovecii pneumonia (PJP) in humans. PJP is treated with trimethoprim-sulfamethoxazole (TMP-SMX), a strong broad-spectrum antibiotic that carries risk of renal and hepatotoxicity. Therefore, rapid diagnosis or exclusion of PJP is crucial to ensure PJP-positive patients receive effective treatment and PJP-negative patients avoid unnecessary antibiotics. Unlike most microorganisms, P. jirovecii cannot be cultured, presenting complications for the typical methods of diagnosing fungal pathogens. Historically, the gold standard for diagnosis was direct microscopic examination with stains such as methenamine silver and calcofluor white, but this diagnostic technique requires highly skilled …

Effect Of Novel Antimicrobial Compounds On Fungal And Bacterial Pathogens, Megan Wilderman

Honors Program: Senior Projects (Public)

Antimicrobial resistance is a growing concern in medicine¹ leading to a need for the development of novel compounds. Two compounds were tested in this study, 2-hydroxyethylhydrazine (HEH) and para-nitrophenyl-isocyanide (NPIC). HEH targets phosphatidylcholine (PC) production², and NPIC targets mitochondrial function³. Choline (Cho) is a compound that bypasses the inhibition of HEH through the Kennedy pathway.² Two-fold serial dilutions were conducted in 96-well plates to test the sensitivity of different bacteria to HEH and fungi to HEH and NPIC in different media types. A choline condition was also included in the HEH dilutions to test …

Fungal Biodiversity, Microbial Communities, And Ecosystem Function In Non-Perennial Streams, Charles T. Bond

Dissertations

A global majority of steams are non-perennial, drying at some point in time and space. Despite the vital roles that fungi and other microbes play in stream ecosystems, most research on stream microbiomes comes from perennial (continuously flowing) streams. The present series of studies addresses this research gap by examining microbial community composition and function in non-perennial streams, with an emphasis on fungi. Chapter I reviews existing scientific literature on the ecological processes that shape microbiome structure and function in non-perennial streams and outlines the varieties of fungi that may live there. Chapter II uses rDNA metabarcoding to survey fungal …

Increased Fungal Burden In The Gastrointestinal Tract Of Brain-Dead Organ Donors, Erika J Nachman, Colleen K Ardis, A Kyle B Ardis, Javier Nieto, Madeline M Bresson, Clare M Robertson, Maggie N Seale, Nora M Villafuerte, Zhe Lyu, Eva C Preisner, Heather A Danhof, Sara C Di Rienzi, Yolanda T Becker, Robert A Britton

Faculty, Staff and Students Publications

Approximately 3% of organ transplant recipients will be diagnosed with an invasive fungal infection (IFI), with 10%-47% being fatal. The source of IFI is typically not known, but Candida spp. cause the majority of IFI cases. We obtained intestines from two types of organ donors, brain-dead (BD) (n = 7) and donation after circulatory death (DCD) (n = 5), to sample microbes from the mucosal surface and the lumen. BD donors were parenterally fed and treated with corticosteroids in the days before procurement, whereas DCD donors were enterally fed and not given corticosteroids. We found fungi present in …

A Toi Rna Editing In Three Members Of The Microbotryum Violaceum Fungal Complext And Characterization Of Adar Genes Of Microbotryum Superbum., Shikhi Baruri

Electronic Theses and Dissertations

A-to-I RNA editing is a process that occurs post-transcriptionally. Through this process, adenosine (A) is replaced by inosine (I) in RNAs by adenosine deaminase enzymes that act on the single-stranded RNA. These enzymes, also known as ADARs, act on RNA. The translation and splicing mechanisms subsequently interpret inosine as guanosine (G), which effectively alters genetic information. This kind of RNA alteration can cause both nonsynonymous and synonymous changes in codon, which may have an impact on protein function. A group of over 89 basidiomycete fungal species known as the Microbotryum violaceum complex infects a similarly large group of plant host …

Investigating Arbuscular Mycorrhizal Fungi-Cover Crop Interactions To Improve Sustainable Agricultural Practices, Isabel M. Zanartu, Connor Morozumi, Natalie Christian

The Cardinal Edge

Arbuscular mycorrhizal fungi (AMF) are fungal species that form beneficial relationships with plants. AMFs are known to help crops acquire important nutrients like nitrogen and phosphorus in the soil, and in return the plants provide carbon to the fungi. At least 80% of all plants partner with AMFs including staple crops such as rice, corn, wheat and soybeans. With so many plants likely relying on AMFs, current farming practices such as planting in monocultures and fallow overwintering may limit these relationships. On top of this, climate change challenges the reliability of these practices in the future. One sustainable agricultural practice …

Targeting Aspergillus Fumigatus Hypoxia Response Pathways For Novel Antifungal Drug Development., Cecilia Gutierrez Perez

Dartmouth College Ph.D Dissertations

Invasive fungal disease present are difficult to diagnose and treat and present a high mortality rate across the world with approximately 1.5 million people a year succumbing to fungal infections worldwide. Currently, there are limited antifungal classes used therapeutically, and antifungal drug resistance on the rise further exacerbates the dire need for novel therapeutics with innovative mode of actions. The filamentous fungi, Aspergillus fumigatus is the causative agent of invasive pulmonary aspergillosis (IPA). It is estimated that contemporary antifungals fail in about 50% of patients with invasive filamentous fungal infections, likely due to the biofilm mode of growth exhibited in …

Microbial Phosphate Solubilization Mechanisms In P Solubilizing In Andisol, Agustina Erlinda Marpaung, Tengku Sabrina, Abdul Rauf, Dwi Ningsih Susilowati, Luthfi Aziz Mahmud Siregar

Jurnal Kultivasi

Phosphate (P) nutrient plays a significant role in plant growth and yield. P is an essential element that plays an important role in photosynthesis and root development. Phosphate nutrient availability is deficient in some soil types due to retention, such as in Andisol soil types. High phosphate retention in Andisol soil types causes P nutrients to be unavailable to plants and can reduce crop yields. The availability of P in Andisol soils can be done, among others, by applying phosphate solubilizing microbes. Phosphate solubilizing microorganisms are soil microorganisms consisting of bacteria and fungi that can mineralize organic P, dissolve inorganic …

Fungal Activity In Fusarium Keratoplasticum Isolates With And Without Endohyphal Bacteria On Various Carbon Sources, Maya Brown

Honors College Theses

In recent years, the fungus Fusarium keratoplastic has been associated with failed sea turtle eggs. One fungal isolate collected from a failed egg collected on Wassaw Island, GA in 2020 contained endohyphal bacteria, bacteria living within the hyphae of the fungus. The type of endohyphal bacteria (EHB), as well as the relationship between the bacteria and fungal hosts, are currently unknown. Previous research on the same fungus and EHB, specifically Chitinophaga sp., discovered that EHB influenced the ability of the fungus to utilize carbon sources. Our research goal was to examine the metabolic relationship of Fusarium isolated from failed sea …

Synthesis, Characterization And Antimicrobial Properties Of Mixed-Ligand Complexes Of Some Metal(Ii) Ions With Barbituric Acid And 1,10-Phenanthroline Ligands, Kayode Taiwo Ishola, Oluwabiyi James Olaoye, Mary Adelaide Oladipo, Omobola Ajibike Odedokun, Oyebanji Oluseun Aboyeji

Tanzania Journal of Science

Many pathogenic organisms have developed resistance to many antibiotics, which leads to an increase in the spread of many microbial infections. There is an urgent need to find more effective drugs to curb widespread transmission. Hence, this study synthesized and evaluated the antimicrobial activities of mixed-ligand complexes of Cu(II), Co(II), Ni(II), Mn(II), and Zn(II) ions with barbituric acid and 1,10 phenanthroline ligands in effort to find more effective antibiotics. The complexes were characterized using elemental analysis, metal analysis, melting points, solubility tests, and spectroscopic analyses (IR and UV-visible). The antimicrobial activities of the complexes were evaluated against two gram-positive bacteria …

Considerations For The Use Of Mycorrhizal Fungi Inoculants In Coal Mine Reclamation And Reforestation In Appalachia: A Guide Of Best Practices And Management Recommendations, Cole Hansen Reistrup

Master's Projects and Capstones

Nearly all terrestrial plants form symbiotic relationships with mycorrhizal fungi. These beneficial soil microbes support plant health by increasing plants’ access to nutrients and water, protecting them from pathogens, improving soil properties, and more. A challenge to restoring forests on coal mined land in Appalachia is that mine soils are often degraded in a number of ways, including lacking mycorrhizal fungi, which makes mine soils difficult for trees to grow upon. Substantial improvements to coal mine reforestation success have been made since the development of the Forestry Reclamation Approach in 2005 that provides guidelines for how to create a suitable …

Do The Culturable Microbial Groups Present In Cutaway Bogs Change According To Temporal Variation? Pilot Study Based On The Midlands In The Republic Of Ireland, Gouri Atapattu, Tara Battersby, Michelle Giltrap, Furong Tian Nanolab Research Centre, Focas Research Institute, Technological University Dublin

Articles

Cutaway peatlands in the midlands of the Republic of Ireland are rarely the focus of scientific studies. The soil quality and related microenvironment have been severely impacted by peat extraction. Returning them to a ‘near-natural state’ would require greater insights into this ecological niche. The current research took the initiative to study the microbiology of vast cutaway sites in the midlands of Ireland. Peat was collected over two seasons in January, February and April. Homogenised peat was aseptically cultured on a range of specific and non-specific culture media. Microbial enumeration, Gram staining and other microscopic observations of morphologically distinct microorganisms …

Temporal Changes In Gastrointestinal Fungi And The Risk Of Autoimmunity During Early Childhood: The Teddy Study, Thomas A Auchtung, Christopher J Stewart, Daniel P Smith, Eric W Triplett, Daniel Agardh, William A Hagopian, Anette G Ziegler, Marian J Rewers, Jin-Xiong She, Jorma Toppari, Åke Lernmark, Beena Akolkar, Jeffrey P Krischer, Kendra Vehik, Jennifer M Auchtung, Nadim J Ajami, Joseph F Petrosino

Faculty, Staff and Students Publications

Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over …

Discovering Novel Polyextremotolerant Fungi And Determining Their Ecological Role Within The Biological Soil Crust Consortium, Erin C. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

The ecological niche of polyextremotolerant fungi within oligotrophic ecosystems such as biological soil crusts has not yet been determined. These fungi persist in locations where nutrients are depleted while simultaneously surrounded by autotrophic microbes such as algae and cyanobacteria. Yet it has not been shown that they are engaging in any exchange of nutrients the way lichens do. However, there is seemingly no other way for these fungi to obtain vital nutrients, such as carbon or nitrogen, other than from these microbes. Here we have isolated polyextremotolerant fungi from cold desert biological soil crusts which are a microbial biofilm that …

Nitrogen Availability In Dune Systems And Its Effect On Root Fungal Endophyte Communities., Haley E. Sage

College of Arts & Sciences Senior Theses

As global change persists, changes in resource availability can influence plant-microbe interactions. To understand how resource availability can influence these interactions and species diversity, I focused this research on how varying nitrogen (N) levels affect root endophyte communities in the plant species Ammophila breviligulata, an ecosystem engineer in the dune system. I analyzed the relationship between nitrogen addition and microbial community composition across 60 plots treated with three nitrogen addition levels (control, low, and high) in a long-term experimental field site in the Lake Michigan dunes. I identified Ammophila breviligulata's root endophyte community after creating a culture collection and …

Functional Characterization Of A Putative Alternative Oxidase In Sporisorium Reilianum F. Sp. Zeae., Emma A Lamb

College of Arts & Sciences Senior Theses

Sporisorium reilianum is a pathogenic basidiomycete fungus with two formae speciales, each capable of infecting corn (SRZ) or sorghum (SRS), respectively. This fungus is also a dimorphic variety, meaning it can switch between its haploid, yeast-like sporidia and diploid teliospore stages over the course of its life cycle (Schirawski). When S. reilianum is found in a haploid state and conditions are favorable, it will mate with a compatible non-self mating type to begin filamentous growth and proliferation in the plant host (Zhao). S. relianum, like most fungi, utilizes the four classical components of the electron transport chain to produce …

Structural Polymorphism Of Chitin And Chitosan In Fungal Cell Walls From Solid-State Nmr And Principal Component Analysis, Liyanage D. Fernando, Malitha C. Dickwella Widanage, Jackson Penfield, Andrew S. Lipton, Nancy Washton, Jean Paul Latgé, Ping Wang, Liqun Zhang, Tuo Wang

School of Graduate Studies Faculty Publications

Chitin is a major carbohydrate component of the fungal cell wall and a promising target for novel antifungal agents. However, it is technically challenging to characterize the structure of this polymer in native cell walls. Here, we recorded and compared 13C chemical shifts of chitin using isotopically enriched cells of six Aspergillus, Rhizopus, and Candida strains, with data interpretation assisted by principal component analysis (PCA) and linear discriminant analysis (LDA) methods. The structure of chitin is found to be intrinsically heterogeneous, with peak multiplicity detected in each sample and distinct fingerprints observed across fungal species. Fungal chitin exhibits partial similarity …

Respons Pertumbuhan Pakcoy Terhadap Asam Humat Dan Trichoderma Dalam Media Tanam Pelepah Kelapa Sawit, Ratih Rahhutami, Aline Sisi Handini, Dwi Astutik

Jurnal Kultivasi

Pemanfaatan limbah organik dari perkebunan sebagai media tanam pakcoy (Brassica chinensis L.) diharapkan dapat ditingkatkan dengan penggunaan pupuk organik serta pupuk hayati. Penelitian disusun menggunakan Rancangan Acak Kelompok (RAK) pola faktorial. Faktor pertama adalah dosis asam humat meliputi 1, 3, dan 5 g. Faktor kedua adalah dosis Trichoderma sp., meliputi 50, 100, dan 150 mL. Data yang diperoleh kemudian dianalisis ragam pada taraf nyata 5%. apabila terdapat pengaruh nyata, dilanjutkan dengan uji DMRT. Hasil penelitian menunjukkan bahwa aplikasi asam humat dan Trichoderma sp. memiliki pengaruh mandiri dan tidak terdapat interaksi. Dosis asam humat 3 g per tanaman menghasilkan jumlah daun, …

Investigation Of Dissimilatory Iron Reduction By Exophiala Hkrs030, Zachary Burton

All Theses

Iron (Fe) is the fourth most abundant element in the Earth’s crust and is an essential component in many biological processes. While highly abundant, free iron is not readily available to biological systems since most iron is present in the earth’s crust in the form of ferrous (Fe2+) and ferric (Fe3+) iron minerals. Because of this limited availability, bacteria, plants and fungi have developed diverse ways to safely assimilate and store iron. Bacteria and some fungi have the ability to dissimilate iron. Dissimilatory iron reduction (DIR) is where Fe3+ is reduced to Fe2+ without the cell assimilating the Fe2+ and …

The Inhibition Of Growth Of S. Cerevisiae, U. Maydis, And M. Lychinidis-Dioicae By Apiaecea Plant Extracts, Jackson M Hoffman, Jared Scott, David Schultz Phd

Undergraduate Arts and Research Showcase

The Apiaceae family of plants contains over 3,500 species, many of which are used as food crops: vegetables (carrot, parsnip, celery, etc.), herbs (cilantro, fennel, dill, etc.), and spices (cumin, anise, caraway, etc.). Many spices have been shown to exhibit antimicrobial properties against both bacteria and fungi. We set out to determine if the Apiaceae spice extracts currently used in our lab for anticancer studies exhibit any antimicrobial properties. Ethanolic extracts were made from several Apiaceae seeds: Apium graveolens (celery), Cuminum cyminum (cumin), Anethum graveolens(dill), Foeniculum vulgare (fennel), Coriandrum satvium (coriander), Pimpinella ansium (anise), Trachyspermum ammi (ajwain), Carum carvi …

Determining The Effects Of Imidacloprid On Non-Target Soil Organisms In Hemlock Stands, Braley Burke

Graduate Theses, Dissertations, and Problem Reports (ETD)

The hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae), is an invasive insect that is causing mortality of eastern hemlock trees, Tsuga canadensis, and Carolina hemlock trees, Tsuga caroliniana, across the eastern United States. To protect these ecologically important tree species, a neonicotinoid insecticide, imidacloprid, is commonly used. Imidacloprid is an effective treatment and can remain effective against HWA for four to six years but long-term (≥ one year after application) non-target effects of imidacloprid on forest ecosystems are not well-studied. This study examined terrestrial non-target effects of imidacloprid in hemlock stands with different treatment histories to …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

Assessment Of Grain Safety In Developing Nations, Jose R. Mendoza

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Grains are the most widely consumed foods worldwide, with maize (Zea mays) being frequently consumed in developing countries where it feeds approximately 900 million people under the poverty line of 2 USD per day. While grain handling practices are acceptable in most developed nations, many developing nations still face challenges such as inadequate field management, drying, and storage. Faulty grain handling along with unavoidably humid climates result in recurrent fungal growth and spoilage, which compromises both the end-quality and safety of the harvest. This becomes particularly problematic where there is little awareness about health risks associated with poor …

Spatio-Temporal Dynamics Of Fungal Communities And Their Effects On Plants, Kel Cook

Biology ETDs

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, …

Investigation Of An Elevational Gradient Reveals Strong Differences Between Bacterial And Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata, Kadeem J. Gilbert, Leonora S. Bittleston, Mark Arcebal K. Naive, Anthony E. Kiszewski, Perry Archival C. Buenavente, David J. Lohman, Naomi E. Pierce

Biology Faculty Publications and Presentations

Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and …

Investigation Of An Elevational Gradient Reveals Strong Differences Between Bacterial And Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata, Kadeem J. Gilbert, Leonora S. Bittleston, Mark Arcebal K. Naive, Anthony E. Kiszewski, Perry Archival C. Buenavente, David J. Lohman, Naomi E. Pierce

Publications and Research

Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the …

Genetic And Biochemical Characterization Of Ergot Alkaloid Synthesizing Fungi And Their Symbionts, Matthew Duane Maust

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ergot alkaloids are fungal tryptophan derived toxins which affect mammalian circulation and neurotransmission. These compounds are biosynthesized by a conserved genetic pathway, known as the ergot alkaloid synthesis (EAS) pathway by fungi belonging to the ascomycete families Trichocomaceae and Clavicipitaceae. Several Ipomoea species and related plants in the morning glory family harbor vertically transmitted symbiotic fungi in the genus Periglandula, also members of Clavicipitaceae, that produce ergot alkaloids. Metabolomic analysis of seeds identified a previously uncharacterized glycoside form of the pharmaceutically important ergot alkaloid, ergonovine. Several species belonging to the fungal genus Metarhizium have recently been shown to have the …

Reproduction And Dispersal Of Biological Soil Crust Organisms, Steven D. Warren, Larry L. St. Clair, Lloyd R. Stark, Louise A. Lewis, Nuttapon Pombubpa, Tania Kurbessoian, Jason E. Stajich, Zachary T. Aanderud

Life Sciences Faculty Research

Biological soil crusts (BSCs) consist of a diverse and highly integrated community of organisms that effectively colonize and collectively stabilize soil surfaces. BSCs vary in terms of soil chemistry and texture as well as the environmental parameters that combine to support unique combinations of organisms—including cyanobacteria dominated, lichen-dominated, and bryophyte-dominated crusts. The list of organismal groups that make up BSC communities in various and unique combinations include—free living, lichenized, and mycorrhizal fungi, chemoheterotrophic bacteria, cyanobacteria, diazotrophic bacteria and archaea, eukaryotic algae, and bryophytes. The various BSC organismal groups demonstrate several common characteristics including—desiccation and extreme temperature tolerance, production of various …

Investigation Of Origin And Growth Of Fungi In Coastal Beach Sand, Ruth L. Wright

Honors Theses

In a previous study from this lab (Stevens, Evans, & Aguirre, 2012) yeast colonies were isolated and grown grown from sand collection at pristine, medium use and high use beaches along the grand strand. In that study greater yeast abundance and greater diversity both correlated with higher census of human use, suggesting that some yeast growth of sites was anthropogenic. However the sand matrix itself also varied from very fine, uniform, dark sand at the pristine beach to coarser, color varying, less tightly packed sand at residential and commercial beaches. This suggested an alternative hypothesis to differential colonization and growth …